Sequence
atgc intronic sequence ATGC exonic sequencegtcgctttacttctttgcatcattctgcacctttttttatccatgaatggggtccctttttgtttccttttgttgtgccactttgcaatatttttatctgtatttatcttactcttttatgaactggtcttattgtgtgctgcagGTTATTTTTATTCCTGGTCCAAAAGTATCCATATTGACAATTAAATTGAGGGAAGATGCGTTTCTGATTGTGCAAATCTTGATGTTTGATGTTCATAGGG
Basic information
species | Oryza sativa |
transcript | LOC_Os03g49520.2 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g49520.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G102475_T01 (Zea mays), 3'ss of exon 8
gtcgctttacttctttgcatcattctgcaccttttttta--tccatgaatggggtccctttttgtttccttttgttgtgccactttgcaatatttttatctgtatttatcttactctttt-atgaactggtc--ttattgtgtgctgcagGTTATTTTTATTCCTGGTCCAAAAGTATCCATATTGACAATTAAATTGAGGGAAGATGCGTTTCTGATTGTGCA-AATCTTGATGTTTGATGTTCATAGGG
|| |||| || |||||||||| ||| ||| || ||| ||| | | || ||| || | | | || || || || | ||| | | ||| || ||| ||| ||| | || || ||||| |||||||||||||||||| ||||||||||||| |||||||||||||||||||||||||||||| | || || ||||| | | ||||||||||| || |
gtaactttgctgctttgcatcaatcttcactttaacttagacccaaaacttggaatcctcattttcttcactta--aagctgtttcaca-tgtttatgtagtaattctactctctcgtttgatggatctgttattttctgtgttctgcagGTTATTTTTATTTCTGGTCCAAAAGTGTCCATATTGACAATTAAATTGAGGGAAGATACATT-CTAATTGTATGCAGACCTGATGTTTGATAACTATTAGT
upper sequence: LOC_Os03g49520.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM5G810275_T02 (Zea mays), 3'ss of exon 8
gtcgctttacttctttgcatcattctgcaccttttttta--tccatgaatggggtccctttttgtttccttttgttgtgccactttgcaatatttttatctgtatttatcttactctttt---atgaactggtcttat-tgtgtgctgcagGTTATTTTTATTCCTGGTCCAAAAGTATCCATATTGACAATTAAATTGAGGGAAGATGCGTTTCTGATTGTGCAAATCTTGATGTTTGATGTTCATAGGG--
|| ||||| || |||||||||||||| || || ||| ||| ||| || ||| ||| |||| | || ||| | || ||| | | ||| || | || | || |||| ||| | || | ||||| |||||||||||||||||| ||||||||||||| |||||||||||||||||||||||||||||| | || || ||| |||| | ||||||||||||| ||| |
gtagctttgctgctttgcatcattcttcattttgagttagacccaaaaattggaaccccc---attttctttacataagctg-tttcccatgtttgtg-cagtaattctactatcttgtttgaatgatctgttattttctgtgttctgcagGTTATTTTTATTTCTGGTCCAAAAGTGTCCATATTGACAATTAAATTGAGGGAAGATACATT-CTAATTATGCAGA-CTTGATGTTTGATAACCATTAGTGT
upper sequence: LOC_Os03g49520.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G102475_T02 (Zea mays), 3'ss of exon 8
gtcgctttacttctttgcatcattctgcaccttttttta--tccatgaatggggtccctttttgtttccttttgttgtgccactttgcaatatttttatctgtatttatcttactctttt-atgaactggtc--ttattgtgtgctgcagGTTATTTTTATTCCTGGTCCAAAAGTATCCATATTGACAATTAAATTGAGGGAAGATGCGTTTCTGATTGTGCAAATCTTGATGTTTGATGTTCATAGGG
|| |||| || |||||||||| ||| ||| || ||| ||| | | || ||| || | | | || || || || | ||| | | ||| || ||| ||| ||| | || || ||||| |||||||||||||||||| ||||||||||||| |||||||||||||||||||||||||||||| | || || |||
gtaactttgctgctttgcatcaatcttcactttaacttagacccaaaacttggaatcctcattttcttcactta--aagctgtttcaca-tgtttatgtagtaattctactctctcgtttgatggatctgttattttctgtgttctgcagGTTATTTTTATTTCTGGTCCAAAAGTGTCCATATTGACAATTAAATTGAGGGAAGATACATT-CTAATT-------------------------------
upper sequence: LOC_Os03g49520.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA15G05410.5 (Glycine max), 3'ss of exon 8
gtcgctttacttctttgcatcattctgcacctttttttatccatgaatggggtccctttttgtttccttttgttgtgccactttgcaatatttttatctgtatttatcttactcttttatgaactggtcttattgtgtgctgcagGTTATTTTTATTCCTGGTCCAAAAGTATCCATATTGACAATTAAATTGAGGGAAGATGCGTTTCTGATTGTGCAAATCTTGATGTTTGATGTTCATAGGG---------------------------------
|| | | || | | | | | | | | | | | ||| | | | || ||| || ||| ||| || | | | || |||||||||||||||| | |||||||||||| |||||||| ||| || | | |||||| ||||||| | || ||| | ||| | | | |
-----------------------------gtttgcccttttcaactgtaaactaataatgggcatgagtctatagctagtcccttcaagaactggaa----atctattata-tctgatatcaaataat---gctctgctctgcaggttatttttaattttggtccaaaagtgtccatattcacattttattcagacgaagataagtttctgttcatgtgaattgtagTGTCGAAGCAACTTGATGACTGGATGTTTCCTGCTAATTGCAGGATTTTAG
upper sequence: LOC_Os03g49520.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA15G05410.4 (Glycine max), 3'ss of exon 8
gtcgctttacttctttgcatcattctgcacctttttttatccatgaatggggtccctttttgtttccttttgttgtgccactttgcaatatttttatctgtatttatcttactcttttatgaactggtcttattgtgtgctgcagGTTATTTTTATTCCTGGTCCAAAAGTATCCATATTGACAATTAAATTGAGGGAAGATGCGTTTCTGATTGTGCAAATCTTGATGTTTGATGTTCATAGGG
|| | | || | | | | | | | | | | | ||| | | | || ||| || ||| ||| || | | | || |||||||||||||||| | |||||||||||| |||||||| ||| || | | |||||| ||||||| | || ||| | ||| | | | |
-----------------------------gtttgcccttttcaactgtaaactaataatgggcatgagtctatagctagtcccttcaagaactggaa----atctattata-tctgatatcaaataat---gctctgctctgcagGTTATTTTTAATTTTGGTCCAAAAGTGTCCATATTCACATTTTATTCAGACGAAGATAAGTTTCTGTTCATGTGAATTGTAGTGTCGAAGCAACTTGATG
upper sequence: LOC_Os03g49520.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA08G19640.2 (Glycine max), 3'ss of exon 8
gtcgctttacttctttgcatcattctgcacctttttttatccatgaatggggtccctttttgtttccttttgttgtgccactttgcaatatttttatctgtatttatcttactcttttatgaactggtcttattgtgtgctgcagGTTATTTTTATTCCTGGTCCAAAAGTATCCATATTGACAATTAAATTGAGGGAAGATGCGTTTCTGATTGTGCAAATCTTGATGTTTGATGTTCATAGGG
||| | || | | | | | | | | | | | ||| | | | || ||| || ||| ||| || | | ||| | |||||||||||||||| | |||||||||||| |||||||| ||| || | | |||||| ||||||| | || ||| | |||| | | | |
--------------------------------gtttgcccttttcaactgtaagctaatgggcctgagtctatagctagtcccttcaagaactggac----atctattata-tctgatatcaaataatgctat---gctctgcagGTTATTTTTAATTTTGGTCCAAAAGTGTCCATATTCACATTTTATTCAGACGAAGATAAGTTTCTGTTCATGTGAATTGTAGTGTTGAAGCAACTTGATGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|29646297|gb|CB651304.1|CB651304EST: TTATACATGCAGTGGGCTGAGCATCACAAAAAGCTGTCCAATTTCTTAAG GTTATTTTTATTCCTGGTCCAAAAGTATCCATATTGACAATTAAATTGAGG
genomic: TTATACATGCAGTGGGCTGAGCATCACAAAAAGCTGTCCAATTTCTTAAGgtcgctttac ... tgtgctgcagGTTATTTTTATTCCTGGTCCAAAAGTATCCATATTGACAATTAAATTGAGG
EST:
gi|58598663|gb|CK009191.1|CK009191EST: GGCTGAGCATCACAAAAAGCTGTCCAATTTCTGAAG GTTATTTTTATTCCTGGTCCAAAAGTATCCATATTGACAATTAAATTGAGG
genomic: GGCTGAGCATCACAAAAAGCTGTCCAATTTCTTAAGgtcgctttac ... tgtgctgcagGTTATTTTTATTCCTGGTCCAAAAGTATCCATATTGACAATTAAATTGAGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttttatctgtatttatcttactcttttatgaactggtcttattgtgtgctgcagGTTATTTTTATTCCTGGTCCAAAAGTATCCATATTGACAATTAAATTGAGGGAAGATGCGTTTCTGATTGTGCAAATCTTGATGTTTGATGTTCATAGGG
atcttac putative branch site (score: 3)
tatttatctta TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcgctttacttctttgcatcattctgcacctttttttatccatgaatggggtccctttttgtttccttttgttgtgccactttgcaatatttttatctgtatttatcttactcttttatgaactggtcttattgtgtgctgcagGTTATTTTTATTCCTGGTCCAAAAGTATCCATATTGACAATTAAATTGAGGGAAGATGCGTTTCTGATTGTGCAAATCTTGATGTTTGATGTTCATAGGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG